{"files"=>["https://ndownloader.figshare.com/files/1476330"], "description"=>"<p>In 1954, a fly population derived from one pair of Oregon-R-S flies was divided into 6 populations. Three of them (aL, bL and cL populations) were reared in normal light-dark cycling conditions and the remaining three populations (dD, eD, and fD populations) were reared in constant dark conditions. Unfortunately, all of the L lines were lost by 2002. The dD and eD lines were lost in 1965 and 1967, and only the fD line has been maintained until now. In 2008, we started to rear the fD line and designated it “Dark-fly”. We have maintained Dark-fly in a minimum medium as done before (black lines), and in a standard cornmeal medium (white lines) in parallel. The population size of Dark-fly has not been controlled but has usually been about 100 flies each in several culture vials.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>1008752, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033288.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_History_of_Dark_fly_/1008752", "title"=>"History of Dark-fly.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-14 06:55:41"}

{"files"=>["https://ndownloader.figshare.com/files/1476350", "https://ndownloader.figshare.com/files/1476351", "https://ndownloader.figshare.com/files/1476352", "https://ndownloader.figshare.com/files/1476353", "https://ndownloader.figshare.com/files/1476354", "https://ndownloader.figshare.com/files/1476355", "https://ndownloader.figshare.com/files/1476356", "https://ndownloader.figshare.com/files/1476357", "https://ndownloader.figshare.com/files/1476358", "https://ndownloader.figshare.com/files/1476359", "https://ndownloader.figshare.com/files/1476360", "https://ndownloader.figshare.com/files/1476361", "https://ndownloader.figshare.com/files/1476362", "https://ndownloader.figshare.com/files/1476363"], "description"=>"<div><p>Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a <i>Drosophila melanogaster</i> line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.</p> </div>", "links"=>[], "tags"=>["genome", "reared"], "article_id"=>1008765, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Minako Izutsu", "Jun Zhou", "Yuzo Sugiyama", "Osamu Nishimura", "Tomoyuki Aizu", "Atsushi Toyoda", "Asao Fujiyama", "Kiyokazu Agata", "Naoyuki Fuse"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033288.s001", "https://dx.doi.org/10.1371/journal.pone.0033288.s002", "https://dx.doi.org/10.1371/journal.pone.0033288.s003", "https://dx.doi.org/10.1371/journal.pone.0033288.s004", "https://dx.doi.org/10.1371/journal.pone.0033288.s005", "https://dx.doi.org/10.1371/journal.pone.0033288.s006", "https://dx.doi.org/10.1371/journal.pone.0033288.s007", "https://dx.doi.org/10.1371/journal.pone.0033288.s008", "https://dx.doi.org/10.1371/journal.pone.0033288.s009", "https://dx.doi.org/10.1371/journal.pone.0033288.s010", "https://dx.doi.org/10.1371/journal.pone.0033288.s011", "https://dx.doi.org/10.1371/journal.pone.0033288.s012", "https://dx.doi.org/10.1371/journal.pone.0033288.s013", "https://dx.doi.org/10.1371/journal.pone.0033288.s014"], "stats"=>{"downloads"=>8, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Features_of_Dark_Fly_a_Drosophila_Line_Reared_Long_Term_in_a_Dark_Environment/1008765", "title"=>"Genome Features of “Dark-Fly”, a <i>Drosophila</i> Line Reared Long-Term in a Dark Environment", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-14 06:55:41"}